met4j merge requestshttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests2022-04-19T15:09:49+02:00https://forgemia.inra.fr/metexplore/met4j/-/merge_requests/9Expand Toolbox with SBML scrapping app2022-04-19T15:09:49+02:00Clement FrainayExpand Toolbox with SBML scrapping appAllows user to extract and format data encapsulated in SBML filesAllows user to extract and format data encapsulated in SBML filesClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/8handling mutliple compartments in side compound scan2022-04-01T17:43:22+02:00Clement Frainayhandling mutliple compartments in side compound scanThis is aimed at improving side compound detection when using models with compartments. The traditional filter by degree often removes H2O and other cofactors from cytosol, but those compounds usually remains in compartments with fewer ...This is aimed at improving side compound detection when using models with compartments. The traditional filter by degree often removes H2O and other cofactors from cytosol, but those compounds usually remains in compartments with fewer biochemical activities, thus with lower overall degree for their constituentsClement FrainayClement Frainayhttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/7Feature/extract sub reaction net2022-02-22T17:01:30+01:00Clement FrainayFeature/extract sub reaction netExtract reaction graph subnetwork (union of shortest paths or steiner tree) from lists of sources reactions and target reactions, analog to existing subgraph extraction on the compound graph. This version do not have default weighting sc...Extract reaction graph subnetwork (union of shortest paths or steiner tree) from lists of sources reactions and target reactions, analog to existing subgraph extraction on the compound graph. This version do not have default weighting scheme, thus requires a file of side compoundsLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/6Remove equals overriding of BioEntity and protects creation of BioParticipant2022-01-25T16:27:58+01:00Ludovic CottretRemove equals overriding of BioEntity and protects creation of BioParticipant- Two bioentity were equals if they had the same id. Now, the two objects must be equal.
- Constructors of BioEnzymeParticipant and BioReactant are now "protected". This avoids to create redundant participants. A BioCollection for each o...- Two bioentity were equals if they had the same id. Now, the two objects must be equal.
- Constructors of BioEnzymeParticipant and BioReactant are now "protected". This avoids to create redundant participants. A BioCollection for each one has been created in the BioNetwork
- The constant parameter is not saved anymore when loading a SBML file. It's not used in Met4j applications. If we want to save reactant attributes, we have to do at the reaction level now.Ludovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/5skip coverage deploy2021-12-16T12:14:40+01:00Ludovic Cottretskip coverage deployLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/4remove coverage from the cache in ci2021-12-16T11:37:41+01:00Ludovic Cottretremove coverage from the cache in ciLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/3Add coverage module2021-12-06T15:56:14+01:00Ludovic CottretAdd coverage moduleFrom https://cylab.be/blog/97/compute-code-coverage-for-a-multi-module-maven-project-with-jacocoFrom https://cylab.be/blog/97/compute-code-coverage-for-a-multi-module-maven-project-with-jacocoLudovic CottretLudovic Cottrethttps://forgemia.inra.fr/metexplore/met4j/-/merge_requests/2[io] handle indentifiers.org urls with https2021-11-26T13:50:19+01:00Clement Frainay[io] handle indentifiers.org urls with httpsXref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in ...Xref parsing from sbml only accept valid identifiers.org uri.
Since they changed from http to https, the validity check has been modified accordingly, accepting both http and https uri.
The default base uri has been switched to https in met4J too, so change has been made to the unit tests.
However, please note that a sbml with http://identifiers.org uris will have them converted to https after exportLudovic CottretLudovic Cottret